RWC; "what is the baseline to determine where one person's rights end and another begins"
Tangible harm. Easy. If a there is a consensus of opinion that an action infringes someones rights to the extent there is tangible harm, then it's 'wrong'.
"Also, if that baseline is based upon nothing more than majority rules than it will change all of the time. For example for far to long we in the states allowed the majority to discriminate upon the minority simply because of the color of their skin. That didn't change because of the change in the majoroty, but because of the religious beliefs of a few that risked their lives."
RWC, you don't mean to be offensive, but you are; "because of the religious beliefs of a few that risked their lives". So I suppose that no religous people supported the US's old race laws. Or Apartheid in South Africa? And that no atheists fought against racial discrimination? You are sooooooooooo biased!! I'm saying this with a smile, not with a frown and a wagging finger, as I really don't think you realise the massive presumptions you make at every turn with regard to theists and atheists.
But to address your concern;
"if that baseline is based upon nothing more than majority rules than it will change all of the time"
Yup, it will. But murder and rape are unlikely to become acceptable again, and have almost always been social taboos to one extent or the other.
As Martin Luther King said "The slow curve of humanity is toward justice". Terrible things - racial and sexual oppression for example - have been socially acceptable (and recall please this was in theistic societies who 'should have known better' as they had is all written down for them). But, over time, things are getting better.
Now sexual and racial oppresion are widely rejected. And the baseline will continue to change; for example, look at sex.
Fifty years ago sex before marriage was widely condemned, single parenthood a shame, and homosexuality a perversion. Now sex before marriage is common, single parenthood is single parenthood, and homosexuality is widely considered no more an indication of someones goodness or badness than their hairstyle.
Of course, if you are taking your morals from a bronze-age goatherd, and have to take his condemnation of sex before marriage and homosexuality (if that's what is was), then you cannot adjust your morals to a modern world which realises that, scientifically speaking, homosexuality is something quite natural, and that sex before marriage is okay as it doesn't have to result in babies now, and that women are not chattel anymore, so treating them like that is hardly appropriate.
So, the fact that morals can and do change is a GOOD thing; do you want to stone adulterers in the local Mall each Saturday? Or throw out all the cotton-polyester blend clothes you have?
"But for a person that claims to be religious, the moral code that he claims to live by is outlined in the Bible so all can see where he falls short."
Again, you presume that 'religious' people regard the 'Bible' as the be all and end all. What about Hindus, Seikhs, Muslims, Buhddists? You know, the majority of the world population? And has the fact the Bible is written doen stopped people who claim to follow it breaking those commandments? And isn't it just as possible to point out, using secular laws, where someone has done wrong?
Xander; Oh, I agree; people have rights, but they also have the right to get over it. Thus people whimpering because they don't like the Mapplethorpe with the bullwhip coming out of a guy's ass can get a sense of perspective. I alsways love it; you get people who will defend a bigot's rights to say what they believe who will complain about bad language...!
People living in glass paradigms shouldn't throw stones...